Research workbench
Structure of the D-erythrose-4-phosphate dehydrogenase from E.COLI in complex with a NAD cofactor analog (3- chloroacetyl adenine pyridine dinucleotide) and sulfate anion
Analyse Structure of the D-erythrose-4-phosphate dehydrogenase from E.COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XF8
- Type
- protein
- Length
- 5,155 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-erythrose-4-phosphate dehydrogenase
- EC
- 1.2.1.72
- UniProt
- P0A9B6
- Ligands
- 3CD, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 10 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 326 | 32% helix, 29% strand | P0A9B6 |
| B, F, J, N | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 325 | 32% helix, 29% strand | P0A9B6 |
| C, G | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 324 | 33% helix, 29% strand | P0A9B6 |
| D, H, P | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 317 | 32% helix, 30% strand | P0A9B6 |
| E | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 325 | 32% helix, 30% strand | P0A9B6 |
| I | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 323 | 33% helix, 28% strand | P0A9B6 |
| K | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 320 | 31% helix, 29% strand | P0A9B6 |
| L | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 316 | 33% helix, 29% strand | P0A9B6 |
| M | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 327 | 32% helix, 28% strand | P0A9B6 |
| O | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 319 | 34% helix, 28% strand | P0A9B6 |
Ligands and binding sites
- 3CD · 3-(chloroacetyl) pyridine adenine dinucleotide · ligand · 8 copies · chains A, C, H, B, E, G, I, K, P, M, O
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.78 | 0.81 | 104 | SO4 |
| 2 | 934 | 0.75 | 0.78 | 93 | SO4, 3CD |
| 3 | 527 | 0.72 | 0.81 | 51 | empty |
| 4 | 1092 | 0.72 | 0.75 | 111 | SO4 |
| 5 | 869 | 0.71 | 0.76 | 113 | SO4, 3CD |
Interfaces
41 interfaces between chains.
- I–J · 2059 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2043 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2034 Ų buried · 30 hydrogen bonds · protein-protein
- M–N · 2021 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1868 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2XF8 · Structure of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli in complex with a NAD… · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A9B6
- Elsewhere: RCSB PDB 2XF8 · PDBe 2XF8 · UniProt P0A9B6
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